Cutting holes into a flat surface
There are several ways to go about this, most common and easiest is to use a boolean modifier. Select the plane and add a Boolean modifier to it, In hte Object field, select the object you want to stamp holes with (ie some cylinders joined together) and change the Operation to Difference. Next apply the modifer, delete or hide the cyclinders then Tab into Edit mode and box select the botton half of the mesh that protruded down and delete these.



If your mesh has thickness, you can just delete or hide the cylinders after applying the boolean modifier.



You can also further read up on some more techniques here http://www.blendernation.com/2013/07/14/8-methods-of-cutting-holes/.